Sun Oct 9 13:59:00 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 13:59:00 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6967960 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -5.788000 44.23000 ymin,ymax (A): 22.48700 73.57800 zmin,zma (A): 41.73100 84.46500 x,y,z range (A): 50.01800 51.09100 42.73400 scale (grids/A): 0.6967960 object centre (A): 19.22100 48.03250 63.09800 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 4.500021 assigned positive charge : 370.6362 centred at (gu) : 89.41863 91.09395 90.58210 assigned negative charge : -366.1365 centred at (gu) : 89.41228 91.26745 90.65073 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7858 nv = 96 ne = 84 npr = 48061 no. pairs analyzed = 48061 no. exposed pairs = 2938 no. arc points = 20670 no. surface atoms = 993 nbur = 1404 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 514 mr = 4374 m= 4 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1966 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5007849E-08 -1.1360688E-09 midg,1,midg; midg,igrid,midg 8.7170861E-08 -6.2629766E-08 1,midg,midg; igrid,midg,midg 3.1001768E-08 3.0003068E-08 gauss-seidel spectral radius is 0.9893011 estimated iterations to convergence 79 setup time was (sec) 0.4800000 now iterating at: 13:59:01 rms-change max change #iterations 0.2071783 30.71029 at 10iterations 2.5748357E-02 4.375608 at 20iterations 3.6949681E-03 0.4854507 at 30iterations 8.3290716E-04 0.1202621 at 40iterations 2.7182160E-04 4.1675568E-02 at 50iterations finished qdiffx linear iterations at : 13:59:03 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 2.7182160E-04 4.1675568E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 13:59:04 3.097u 0.149s 0:03.51 92.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 13:59:04 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.090388 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -5.788000 44.23000 ymin,ymax (A): 22.48700 73.57800 zmin,zma (A): 41.73100 84.46500 x,y,z range (A): 50.01800 51.09100 42.73400 scale (grids/A): 2.090388 object centre (A): 19.22100 48.03250 63.09800 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 4.500021 assigned positive charge : 370.6362 centred at (gu) : 88.25552 93.28146 91.74586 assigned negative charge : -366.1365 centred at (gu) : 88.23666 93.80209 91.95190 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 83395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20670 grid for indexing accessible points = 1.400000 m= 32260 mr = 58149 m= 6012 mr = 24095 m= 562 mr = 3982 m= 9 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.6500000 number of dielectric boundary points 35710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17894 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6967960 object centre at (A) : 19.22100 48.03250 63.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3923128E-02 1.2200350E-02 midg,1,midg; midg,igrid,midg 1.3704367E-02 -5.1385865E-02 1,midg,midg; igrid,midg,midg 6.6668458E-02 1.0322622E-02 gauss-seidel spectral radius is 0.9988384 estimated iterations to convergence 232 setup time was (sec) 0.9100000 now iterating at: 13:59:05 rms-change max change #iterations 5.037420 234.8558 at 10iterations 2.488505 91.19736 at 20iterations 1.237246 35.46061 at 30iterations 0.6130732 19.49812 at 40iterations 0.3055783 9.095041 at 50iterations 0.1526366 4.087062 at 60iterations 7.5722016E-02 2.260170 at 70iterations 3.7814483E-02 1.064962 at 80iterations 1.9048119E-02 0.5428238 at 90iterations 9.6963448E-03 0.3024654 at 100iterations 5.0012479E-03 0.1373710 at 110iterations 2.7019363E-03 8.5769653E-02 at 120iterations finished qdiffx linear iterations at : 13:59:11 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 2.7019363E-03 8.5769653E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 13:59:11 7.047u 0.175s 0:07.51 96.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 13:59:11 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.135582 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -5.788000 44.23000 ymin,ymax (A): 22.48700 73.57800 zmin,zma (A): 41.73100 84.46500 x,y,z range (A): 50.01800 51.09100 42.73400 scale (grids/A): 3.135582 object centre (A): 19.22100 48.03250 63.09800 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 4.500021 assigned positive charge : 370.6362 centred at (gu) : 87.38315 94.92208 92.61877 assigned negative charge : -366.1365 centred at (gu) : 87.35500 95.70299 92.92769 start vw surface at 0.1300000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 192103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20670 grid for indexing accessible points = 1.400000 m= 101625 mr = 140351 m= 40104 mr = 83642 m= 11271 mr = 32667 m= 2368 mr = 8675 m= 280 mr = 1821 m= 3 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 336 time to turn everything in is 1.830000 number of dielectric boundary points 80413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 18048 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.090388 object centre at (A) : 19.22100 48.03250 63.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6170930 1.6431162E-02 midg,1,midg; midg,igrid,midg 0.3517703 -0.5536304 1,midg,midg; igrid,midg,midg 0.7531239 -0.1199452 gauss-seidel spectral radius is 0.9993019 estimated iterations to convergence 299 setup time was (sec) 2.120000 now iterating at: 13:59:14 rms-change max change #iterations 11.21713 368.1125 at 10iterations 6.664992 134.0528 at 20iterations 3.936893 84.08817 at 30iterations 2.327269 44.68528 at 40iterations 1.377660 26.17138 at 50iterations 0.8075738 13.41759 at 60iterations 0.4754939 8.274839 at 70iterations 0.2797796 4.734879 at 80iterations 0.1645505 2.978216 at 90iterations 9.6685126E-02 1.737397 at 100iterations 5.6781568E-02 0.9375572 at 110iterations 3.3556439E-02 0.6002960 at 120iterations 2.0014573E-02 0.3258209 at 130iterations 1.2119805E-02 0.2252655 at 140iterations 7.5585805E-03 0.1445389 at 150iterations 4.9495157E-03 0.1014938 at 160iterations 3.4335514E-03 7.5157166E-02 at 170iterations 2.5520527E-03 5.6495667E-02 at 180iterations finished qdiffx linear iterations at : 13:59:23 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 2.5520527E-03 5.6495667E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 13:59:24 11.766u 0.174s 0:12.20 97.7% 0+0k 0+0io 0pf+0w